EP3068904A4 - Systems and methods for universal tail-based indexing strategies for amplicon sequencing - Google Patents

Systems and methods for universal tail-based indexing strategies for amplicon sequencing Download PDF

Info

Publication number: EP3068904A4
Authority: EP; European Patent Office
Prior art keywords: systems; methods; amplicon sequencing; based indexing; universal tail
Prior art date: 2013-11-11
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.): Withdrawn

Application number

EP14860102.4A

Other languages

German (de)

French (fr)

Other versions

EP3068904A2 (en

Inventor

James M. Schupp

Rebecca Colman

David Engelthaler

John GILLECE

Nathan HICKS

Paul S. Keim

Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)

Northern Arizona University

Translational Genomics Research Institute TGen

Original Assignee

Northern Arizona University

Translational Genomics Research Institute TGen

Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)

2013-11-11

Filing date

2014-11-10

Publication date

2017-11-15

2014-11-10 Application filed by Northern Arizona University, Translational Genomics Research Institute TGen filed Critical Northern Arizona University

2016-09-21 Publication of EP3068904A2 publication Critical patent/EP3068904A2/en

2017-11-15 Publication of EP3068904A4 publication Critical patent/EP3068904A4/en

Status Withdrawn legal-status Critical Current

Classifications

- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/686—Polymerase chain reaction [PCR]
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
- C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation

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Chemical & Material Sciences (AREA)
Life Sciences & Earth Sciences (AREA)
Organic Chemistry (AREA)
Proteomics, Peptides & Aminoacids (AREA)
Engineering & Computer Science (AREA)
Zoology (AREA)
Wood Science & Technology (AREA)
Health & Medical Sciences (AREA)
Biophysics (AREA)
General Engineering & Computer Science (AREA)
Immunology (AREA)
Microbiology (AREA)
Molecular Biology (AREA)
Analytical Chemistry (AREA)
Physics & Mathematics (AREA)
Genetics & Genomics (AREA)
Biochemistry (AREA)
Bioinformatics & Cheminformatics (AREA)
Biotechnology (AREA)
General Health & Medical Sciences (AREA)
Chemical Kinetics & Catalysis (AREA)
Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

EP14860102.4A 2013-11-11 2014-11-10 Systems and methods for universal tail-based indexing strategies for amplicon sequencing Withdrawn EP3068904A4 (en)

Applications Claiming Priority (2)

Application Number	Priority Date	Filing Date	Title
US201361902432P	2013-11-11	2013-11-11
PCT/US2014/064890 WO2015070187A2 (en)	2013-11-11	2014-11-10	Systems and methods for universal tail-based indexing strategies for amplicon sequencing

Publications (2)

Publication Number	Publication Date
EP3068904A2 EP3068904A2 (en)	2016-09-21
EP3068904A4 true EP3068904A4 (en)	2017-11-15

Family

ID=53042351

Family Applications (1)

Application Number	Title	Priority Date	Filing Date
EP14860102.4A Withdrawn EP3068904A4 (en)	2013-11-11	2014-11-10	Systems and methods for universal tail-based indexing strategies for amplicon sequencing

Country Status (4)

Country	Link
US (1)	US10550427B2 (en)
EP (1)	EP3068904A4 (en)
AU (1)	AU2014346399A1 (en)
WO (1)	WO2015070187A2 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number	Priority date	Publication date	Assignee	Title
EP4219734A1 (en) *	2015-11-04	2023-08-02	The Translational Genomics Research Institute	Systems and methods of diagnosing and characterizing infections
WO2017139715A1 (en)	2016-02-11	2017-08-17	The Translational Genomics Research Institute	Systems and methods for the detection of infectious diseases
US11248270B2 (en)	2016-03-14	2022-02-15	The Translational Genomics Research Institute	Methods and kits to identify Klebsiella strains
WO2017165864A1 (en) *	2016-03-25	2017-09-28	Karius, Inc.	Synthetic nucleic acid spike-ins
JP7056012B2 (en)	2017-05-19	2022-04-19	トヨタ自動車株式会社	Random primer set and method for preparing a DNA library using it
US11359251B2 (en)	2017-07-21	2022-06-14	The Translational Genomics Research Institute	Methods for the detection of enterovirus D68 in complex samples
JP7047373B2 (en)	2017-12-25	2022-04-05	トヨタ自動車株式会社	Next-generation sequencer primer and its manufacturing method, DNA library using next-generation sequencer primer, its manufacturing method, and genomic DNA analysis method using the DNA library.
US20190323066A1 (en) *	2018-04-20	2019-10-24	Longhorn Vaccines And Diagnostics, Llc	Rapid Methods for the Detection of Microbial Resistance
EP4428234A3 (en)	2018-11-21	2024-09-25	Karius, Inc.	Direct-to-library methods, systems, and compositions
WO2020159977A1 (en)	2019-01-29	2020-08-06	The Translational Genomics Research Institute	Methods and assays for detection and subtyping of microbial pathogens
WO2021183893A1 (en) *	2020-03-13	2021-09-16	The Translational Genomics Research Institute	Methods and kits for the detection of sars-cov-2
WO2021183897A1 (en) *	2020-03-13	2021-09-16	The Translational Genomics Research Institute	Methods and kits for the detection of mers-cov
CN112941214B (en) *	2021-03-29	2023-04-11	中国农业大学	Primer group for gram-negative bacterium drug-resistant gene high-throughput amplicon sequencing and application

Citations (2)

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Publication number	Priority date	Publication date	Assignee	Title
WO2005042759A2 (en) *	2003-09-10	2005-05-12	Althea Technologies, Inc.	Expression profiling using microarrays
US20130137587A1 (en) *	2010-06-09	2013-05-30	Keygene N.V.	Combinatorial sequence barcodes for high throughput screening

Family Cites Families (5)

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Publication number	Priority date	Publication date	Assignee	Title
EP1951901B1 (en) *	2005-10-14	2012-03-07	Cleveland State University	Methods for simultaneously identifying multiple DNA alteration or methylation markers in a large background of wild-type DNA
US7754429B2 (en)	2006-10-06	2010-07-13	Illumina Cambridge Limited	Method for pair-wise sequencing a plurity of target polynucleotides
WO2009126678A2 (en) *	2008-04-08	2009-10-15	Cornell University	Detection of target nucleic acid sequences using fluorescence resonance energy transfer
US8765686B2 (en) *	2010-08-03	2014-07-01	University Of Washington Through Its Center For Commercialization	Polypeptides for treating and/or limiting influenza infection
US9150852B2 (en) *	2011-02-18	2015-10-06	Raindance Technologies, Inc.	Compositions and methods for molecular labeling

2014
- 2014-11-10 EP EP14860102.4A patent/EP3068904A4/en not_active Withdrawn
- 2014-11-10 AU AU2014346399A patent/AU2014346399A1/en not_active Abandoned
- 2014-11-10 US US15/034,544 patent/US10550427B2/en active Active
- 2014-11-10 WO PCT/US2014/064890 patent/WO2015070187A2/en not_active Ceased

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number	Priority date	Publication date	Assignee	Title
WO2005042759A2 (en) *	2003-09-10	2005-05-12	Althea Technologies, Inc.	Expression profiling using microarrays
US20130137587A1 (en) *	2010-06-09	2013-05-30	Keygene N.V.	Combinatorial sequence barcodes for high throughput screening

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
MAHMOOD GHOLAMI ET AL: "A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants : Tailed multiplex 454 amplicon sequencing", PLANT BIOTECHNOLOGY JOURNAL, vol. 10, no. 6, 11 April 2012 (2012-04-11), GB, pages 635 - 645, XP055580965, ISSN: 1467-7644, DOI: 10.1111/j.1467-7652.2012.00696.x *

Also Published As

Publication number	Publication date
WO2015070187A2 (en)	2015-05-14
US20160326572A1 (en)	2016-11-10
WO2015070187A3 (en)	2015-11-19
AU2014346399A1 (en)	2016-06-02
US10550427B2 (en)	2020-02-04
EP3068904A2 (en)	2016-09-21

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Legal Events

Date	Code	Title	Description
2016-08-19	PUAI	Public reference made under article 153(3) epc to a published international application that has entered the european phase	Free format text: ORIGINAL CODE: 0009012
2016-09-21	17P	Request for examination filed	Effective date: 20160602
2016-09-21	AK	Designated contracting states	Kind code of ref document: A2 Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR
2016-09-21	AX	Request for extension of the european patent	Extension state: BA ME
2016-10-12	RIN1	Information on inventor provided before grant (corrected)	Inventor name: ENGELTHALER, DAVID Inventor name: GILLECE, JOHN Inventor name: SCHUPP, JAMES M. Inventor name: KEIM, PAUL S. Inventor name: HICKS, NATHAN Inventor name: COLMAN, REBECCA
2017-02-15	DAX	Request for extension of the european patent (deleted)
2017-07-12	RIC1	Information provided on ipc code assigned before grant	Ipc: C12Q 1/68 20060101AFI20170606BHEP
2017-10-18	A4	Supplementary search report drawn up and despatched	Effective date: 20170914
2017-10-18	RIC1	Information provided on ipc code assigned before grant	Ipc: C12Q 1/68 20060101AFI20170908BHEP
2017-11-15	RA4	Supplementary search report drawn up and despatched (corrected)	Effective date: 20171013
2018-09-26	17Q	First examination report despatched	Effective date: 20180827
2020-01-24	STAA	Information on the status of an ep patent application or granted ep patent	Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN
2020-02-26	18D	Application deemed to be withdrawn	Effective date: 20190924